Literature DB >> 30815087

How Sustainable are Biomedical Ontologies?

James Geller1, Vipina K Keloth1, Mark A Musen2.   

Abstract

BioPortal is widely regarded to be the world's most comprehensive repository of biomedical ontologies. With a coverage of many biomedical subfields by 716 ontologies (June 27, 2018), BioPortal is an extremely diverse repository. BioPortal maintains easily accessible information about the ontologies submitted by ontology curators. This includes size (concepts/classes, relationships/properties), number of projects, update history, and access history. Ontologies vary by size (from a few concepts to hundreds of thousands), by frequency of update/visit and by number of projects. Interestingly, some ontologies are rarely updated even though they contain thousands of concepts. In an informal email inquiry, we attempted to understand the reasons why ontologies that were built with a major investment of effort are apparently not sustained. Our analysis indicates that lack of funding, unavailability of human resources, and folding of ontologies into other ontologies are the most common among several other factors for discontinued maintenance of these ontologies.

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Year:  2018        PMID: 30815087      PMCID: PMC6371329     

Source DB:  PubMed          Journal:  AMIA Annu Symp Proc        ISSN: 1559-4076


  15 in total

1.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

2.  The creation of an ontology of clinical document names.

Authors:  P Frazier; A Rossi-Mori; R H Dolin; L Alschuler; S M Huff
Journal:  Stud Health Technol Inform       Date:  2001

3.  The Protégé Project: A Look Back and a Look Forward.

Authors:  Mark A Musen
Journal:  AI Matters       Date:  2015-06

4.  BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.

Authors:  Patricia L Whetzel; Natalya F Noy; Nigam H Shah; Paul R Alexander; Csongor Nyulas; Tania Tudorache; Mark A Musen
Journal:  Nucleic Acids Res       Date:  2011-06-14       Impact factor: 16.971

5.  The NCBI Taxonomy database.

Authors:  Scott Federhen
Journal:  Nucleic Acids Res       Date:  2011-12-01       Impact factor: 16.971

6.  Disease Ontology: a backbone for disease semantic integration.

Authors:  Lynn Marie Schriml; Cesar Arze; Suvarna Nadendla; Yu-Wei Wayne Chang; Mark Mazaitis; Victor Felix; Gang Feng; Warren Alden Kibbe
Journal:  Nucleic Acids Res       Date:  2011-11-12       Impact factor: 16.971

7.  Controlled vocabularies and semantics in systems biology.

Authors:  Mélanie Courtot; Nick Juty; Christian Knüpfer; Dagmar Waltemath; Anna Zhukova; Andreas Dräger; Michel Dumontier; Andrew Finney; Martin Golebiewski; Janna Hastings; Stefan Hoops; Sarah Keating; Douglas B Kell; Samuel Kerrien; James Lawson; Allyson Lister; James Lu; Rainer Machne; Pedro Mendes; Matthew Pocock; Nicolas Rodriguez; Alice Villeger; Darren J Wilkinson; Sarala Wimalaratne; Camille Laibe; Michael Hucka; Nicolas Le Novère
Journal:  Mol Syst Biol       Date:  2011-10-25       Impact factor: 11.429

8.  ChEBI in 2016: Improved services and an expanding collection of metabolites.

Authors:  Janna Hastings; Gareth Owen; Adriano Dekker; Marcus Ennis; Namrata Kale; Venkatesh Muthukrishnan; Steve Turner; Neil Swainston; Pedro Mendes; Christoph Steinbeck
Journal:  Nucleic Acids Res       Date:  2015-10-13       Impact factor: 16.971

9.  MIRO and IRbase: IT tools for the epidemiological monitoring of insecticide resistance in mosquito disease vectors.

Authors:  Emmanuel Dialynas; Pantelis Topalis; John Vontas; Christos Louis
Journal:  PLoS Negl Trop Dis       Date:  2009-06-23

10.  A survey of SNOMED CT implementations.

Authors:  Dennis Lee; Ronald Cornet; Francis Lau; Nicolette de Keizer
Journal:  J Biomed Inform       Date:  2012-10-03       Impact factor: 6.317

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  1 in total

1.  Developing an ontology for representing the domain knowledge specific to non-pharmacological treatment for agitation in dementia.

Authors:  Zhenyu Zhang; Ping Yu; Hui Chen Rita Chang; Sim Kim Lau; Cui Tao; Ning Wang; Mengyang Yin; Chao Deng
Journal:  Alzheimers Dement (N Y)       Date:  2020-09-01
  1 in total

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